Examples with Measurement io.github.mianalysis.mia.object.Measurement used on opensource projects

Example 21 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class RelateManyToOne method calculateFractionalDistance.

public static void calculateFractionalDistance(Obj childObject, Obj parentObject, double minDist) {
    // Calculating the furthest distance to the edge
    if (parentObject.getMeasurement("MAX_DIST") == null) {
        // Creating an image for the parent object
        Image parentImage = parentObject.getAsImage("Parent", false);
        Image distImage = DistanceMap.process(parentImage, "Distance", true, DistanceMap.WeightModes.WEIGHTS_3_4_5_7, true, false);
        Image projectedImage = ProjectImage.projectImageInZ(distImage, "Projected", ProjectImage.ProjectionModes.MAX);
        double maxDist = projectedImage.getImagePlus().getStatistics().max;
        parentObject.addMeasurement(new Measurement("MAX_DIST", maxDist));
    }
    // Adding measurement
    double maxDist = parentObject.getMeasurement("MAX_DIST").getValue();
    double frac = Math.abs(minDist / maxDist);
    String measurementName = getFullName(Measurements.DIST_CENT_SURF_FRAC, parentObject.getName());
    childObject.addMeasurement(new Measurement(measurementName, frac));
}

Example 22 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class RelateManyToOne method applyLinkMeasurements.

static void applyLinkMeasurements(Objs parentObjects, Objs childObjects) {
    String parentMeasurementName = getFullName(Measurements.WAS_LINKED, childObjects.getName());
    String childMeasurementName = getFullName(Measurements.WAS_LINKED, parentObjects.getName());
    for (Obj parentObject : parentObjects.values()) {
        if (parentObject.getChildren(childObjects.getName()).size() == 0) {
            parentObject.addMeasurement(new Measurement(parentMeasurementName, 0));
        } else {
            parentObject.addMeasurement(new Measurement(parentMeasurementName, 1));
        }
    }
    for (Obj childObject : childObjects.values()) {
        if (childObject.getParent(parentObjects.getName()) == null) {
            childObject.addMeasurement(new Measurement(childMeasurementName, 0));
        } else {
            childObject.addMeasurement(new Measurement(childMeasurementName, 1));
        }
    }
}

Example 23 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class RelateManyToOne method linkByCentroidProximity.

public static void linkByCentroidProximity(Objs parentObjects, Objs childObjects, boolean linkInSameFrame, double linkingDistance, int nThreads) {
    String moduleName = RelateObjects.class.getSimpleName();
    String measurementNamePx = getFullName(Measurements.DIST_CENTROID_PX, parentObjects.getName());
    String measurementNameCal = getFullName(Measurements.DIST_CENTROID_CAL, parentObjects.getName());
    AtomicInteger count = new AtomicInteger(1);
    int numberOfChildren = childObjects.size();
    // Ensuring all parent objects have a calculated centroid
    for (Obj parent : parentObjects.values()) parent.getMeanCentroid();
    ThreadPoolExecutor pool = new ThreadPoolExecutor(nThreads, nThreads, 0L, TimeUnit.MILLISECONDS, new LinkedBlockingQueue<>());
    for (Obj childObject : childObjects.values()) {
        Runnable task = () -> {
            double minDist = Double.MAX_VALUE;
            Obj minLink = null;
            double dpp = childObject.getDppXY();
            for (Obj parentObject : parentObjects.values()) {
                if (linkInSameFrame & parentObject.getT() != childObject.getT())
                    continue;
                double dist = childObject.getCentroidSeparation(parentObject, true);
                if (dist < minDist && dist <= linkingDistance) {
                    minDist = dist;
                    minLink = parentObject;
                }
            }
            // Adding measurements to the input object
            if (minLink != null) {
                childObject.addParent(minLink);
                minLink.addChild(childObject);
                childObject.addMeasurement(new Measurement(measurementNamePx, minDist));
                childObject.addMeasurement(new Measurement(measurementNameCal, minDist * dpp));
            } else {
                childObject.addMeasurement(new Measurement(measurementNamePx, Double.NaN));
                childObject.addMeasurement(new Measurement(measurementNameCal, Double.NaN));
            }
            writeProgressStatus(count.getAndIncrement(), numberOfChildren, "objects", moduleName);
        };
        pool.submit(task);
    }
    pool.shutdown();
    try {
        // i.e. never terminate early
        pool.awaitTermination(Integer.MAX_VALUE, TimeUnit.DAYS);
    } catch (InterruptedException e) {
    // Do nothing as the user has selected this
    }
}

Example 24 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class RelateManyToOne method spatialOverlap.

public void spatialOverlap(Objs parentObjects, Objs childObjects, double minOverlap, boolean centroidOverlap, boolean linkInSameFrame) {
    long nCombined = parentObjects.size() * childObjects.size();
    long count = 0;
    String overlapMeasurementName = getFullName(Measurements.OVERLAP_PC, parentObjects.getName());
    // If there are no objects to link, just set all children to no link
    if (nCombined == 0)
        return;
    // Runs through each child object against each parent object
    for (Obj parentObject : parentObjects.values()) {
        for (Obj childObject : childObjects.values()) {
            // Testing if the two objects are in the same frame (if this matters)
            if (linkInSameFrame && parentObject.getT() != childObject.getT())
                continue;
            // If requiring the child centroid is overlapped with the parent object
            if (centroidOverlap) {
                int xCent = (int) Math.round(childObject.getXMean(true));
                int yCent = (int) Math.round(childObject.getYMean(true));
                // Relates to image location
                int zCent = (int) Math.round(childObject.getZMean(true, false));
                Point<Integer> centroid = new Point<>(xCent, yCent, zCent);
                // If the centroid doesn't overlap, skip this link
                if (!parentObject.contains(centroid))
                    continue;
            }
            // Calculates the percentage overlap
            double nTotal = (double) childObject.size();
            double nOverlap = (double) parentObject.getOverlap(childObject);
            double overlap = (nOverlap / nTotal) * 100;
            // Testing the minimum overlap requirement
            if (overlap == 0 || overlap <= minOverlap)
                continue;
            // If the tests are successful, addRef the link. If the child has already been
            // linked, but with a smaller
            // overlap, remove that link.
            Obj oldParent = childObject.getParent(parentObject.getName());
            if (oldParent != null) {
                if (childObject.getMeasurement(overlapMeasurementName).getValue() < overlap) {
                    oldParent.removeChild(childObject);
                } else {
                    // If the previous link had a better overlap, skip the assignment
                    continue;
                }
            }
            // Creating the link
            parentObject.addChild(childObject);
            childObject.addParent(parentObject);
            // Adding the overlap as a measurement
            Measurement measurement = new Measurement(getFullName(Measurements.OVERLAP_PC, parentObject.getName()));
            measurement.setValue(overlap);
            childObject.addMeasurement(measurement);
        }
        writeStatus("Compared " + Math.floorDiv(100 * childObjects.size() * ++count, nCombined) + "% of pairs");
    }
}

Example 25 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class TrackObjects method getMeasurementCost.

public static double getMeasurementCost(Obj prevObj, Obj currObj, String measurementName) {
    Measurement currMeasurement = currObj.getMeasurement(measurementName);
    Measurement prevMeasurement = prevObj.getMeasurement(measurementName);
    if (currMeasurement == null || prevMeasurement == null)
        return Double.NaN;
    double currMeasurementValue = currMeasurement.getValue();
    double prevMeasurementValue = prevMeasurement.getValue();
    return Math.abs(prevMeasurementValue - currMeasurementValue);
}